Hi,
On Sep 14, 2009, at 6:34 PM, Loren Engrav wrote:
I too would vote for a 1 2 3 set of install instructions
David's post should have all-but-nailed it ... some comments in line:
, maybe for 32bit and 64bit if they differ
They don't. The R that you install following the instructions below is
a universal build, so 32bit and 64 bit (ppc + intel) are all installed.
R is then launched in 32 bit or 64 bit mode by the command line args
sent to it on launch. The various GUI's (if you go that route) take
care of this for you. The 64 bit gui are the ones w/ 64 at the end of
their download link, eg:
* http://r.research.att.com/R-GUI-5426-2.1-leopard-Leopard.dmg (32
bit); vs
* http://r.research.att.com/R-GUI-5426-2.1-leopard-Leopard64.dmg (64
bit)
If you launch R from the terminal, it defaults to 32bit.
If you want to launch R form the terminal in 64bit, you would do:
For intel:
$ R --arch x86_64
For ppc:
$ R --arch ppc64
I did the 123 below and
1-the were many messages during install like " x
Library/Frameworks/R.framework/Versions/2.9/Resources/share/texmf/:
Can't
update time for
Library/Frameworks/R.framework/Versions/2.9/Resources/share/texmf:
Operation
not permitted, but
2-2.9.2 seems to function OK after simple testing; is that warning
insignificant
Long version:
This is because you need to run the "tar" command as a user who has
privileges to write to the directory that the files are being
uncompressed to.
Short version:
2c of David's commands should be:
2. c) click on the Terminal window and
(i) Type (without quotes): "sudo "
(ii) Paste in the tar command: cmd-V to paste-in that command.
So, the command to execute at 2c in your terminal is:
$ sudo tar fvxz R*.tar.gz -C /
I would do this again to ensure you have all of the 2.9.2 "parts" in
there (ie, don't assume that everything was OK when you did it and got
all those "permission denied" warnings/errors).
3-R.app available at http://r.research.att.com/ is 5426 but 5455 32
and 64
bit available at
http://r.research.att.com/R-GUI-5455-2.9-leopard-Leopard.dmg as per
8/6/09
r-sig-mac discussion so I put in 5455; but why 5426 here and 5455
there?
I don't have an answer for that, 5455 is a later build of the .app, so
if it's working for you, I guess just go ahead and keep using that
one. Otherwise, fall back to the one on the site.
Hope that helps some,
-steve
Thank you
Loren Engrav, MD
U Washington
From: David Winsemius <[email protected]>
Date: Mon, 14 Sep 2009 13:00:52 -0400
To: Steve Lianoglou <[email protected]>
Cc: r-help <[email protected]>, ivo welch
<[email protected]>,
"[email protected]" <[email protected]>
Subject: Re: [R-SIG-Mac] [R] 64-bit OSX binary for 2.9.2
On Sep 14, 2009, at 11:59 AM, Steve Lianoglou wrote:
Hi,
On Sep 14, 2009, at 11:44 AM, ivo welch wrote:
dear R wizards: I am looking for a binary package distribution of
R 2.9.2
for OSX . Looking at http://r.research.att.com/ , there seems to
be only a
binary for 2.9.0 . is the 2.9.2 version binary package available
somewhere? (at this point, would it make sense to elevate the 64-
bit
version to a "standard recommended" rather than just a "boutique"
version?)
There isn't a *.pkg / *.dmg install for it, but it's there. In this
section:
Universal nightly builds for Mac OS X (10.4 Tiger and 10.5 Leopard)
Third row in the table:
http://r.research.att.com/R-2.9-branch-leopard-universal.tar.gz
You have to inflate it at the root of your HD. The text right below
the d/l table tells you how to do that:
"""Alternatively you can use the tar-ball (*.tar.gz) which must be
unpacked in the root (e.g. tar fvxz R*.tar.gz -C /), but doesn't
contain the GUI (see below for a separate download)."""
The problem may arise for *NIX-newbies ( a group in which I still
claim membership) that they are unable to operationalize that
message. For one thing they may not even know how to open a Terminal
window. For another they may not know that the "/" at the end of that
command will take care of "unpacking at the root", so they will not
need to navigate away from the place that they find themselves when
Terminal opens up a bash session. The steps broken down would be
something along these lines:
First : Download the nightly build, and select "Save to file" rather
than opening with Stuffit, and then it by default should end up in
the
<user>/Downloads/ folder.
1. a-c) Go to the Utilities folder of the Applications folder and
double-click on Terminal.app
2. a) Go back to the browser and select the string: tar fvxz
R*.tar.gz -C /
(I would solicit some input here from more competent UNIXers
regarding
whether one would ever need to prefix this command with sudo.)
2. b) cmd-C to put it in the clipboard
2. c) click on the Terminal window and cmd-V to paste-in that
command.
2 d) use the arrow and backspace keys (since mouse-clicking does not
change the cursor position in Terminal sessions) to delete the
"R*.tar.gz" on the command line.
3 a) Navigate with the Finder to the Downloads/ folder and locate the
R<build>. Click-drag that file to the Terminal window and
"unclick" (or is it lift-click) when the pointer is at the place on
the command line where the "R*.tar.gz" used to be. A full path
version
of the file name will get inserted (an no quotes are needed, unlike
what one might expect after working in R regularly.)
On my machine, one now sees this on the command line:
tar fvxz /Users/davidwinsemius/Downloads/R-2.9-branch-leopard-
universal.tar.gz -C /
4) Hit <return>
Sit back and watch the show.
You can the separately download the appropriate R-GUI and put in in
the /Applications/ folder.
You'll have to install the R.app GUI separately if you want to use
the 2.9.2 install, otherwise I think the 2.9.0 *.pkg installer
includes it, though I'm not sure.
It does, In fact, it has both the 32 bit GUI and the 64 bit GUI. What
I did was install that package _first_ which gave me 2.9.0 and then
performed the steps above. You really would not want to do it in a
reversed order, since you would be replacing R 2.9.2 with R 2.9.0.
And of course this message _should_ have gone to [email protected]
and any follow up should trim the r-help address.
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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